Pathogen attack of crop plants is a key issue affecting agricultural sustainability in terms of both yield loss due to disease and environmental impact due to fungicide application. The oomycete pathogen Phytophthora infestans is the most significant pathogen of potato, the world's fourth largest crop. P. infestans is responsible for large yield losses through late blight disease, and costs associated with chemical control amount to £3M globally per year. Genetic resistance to P. infestans and control chemicals have been deployed with limited success, as both have been readily overcome by variation in pathogen populations. This proposal aims to address the problems faced by existing control measures through exploitation of the P. infestans genome to seek vital and invariant components of its pathogenicity arsenal that can be targeted for sustainable potato protection. Specifically, this information will be used to identify sources of durable potato disease resistance for breeding and to develop novel control strategies that are intrinsically difficult for the pathogen to overcome. The oomycetes include more than 70 Phytophthora species and are arguably the most significant pathogens of dicotyledenous plants. In the last year or so, genes have been identified from oomycete pathogens of the model plant Arabidopsis, of soybean, and from P. infestans itself (by the SCRI group), that encode proteins that trigger resistance. These proteins are very different to each other except from a conserved motif that is similar to a sequence required for delivery of malaria virulence proteins inside human blood cells. Preliminary evidence suggests that this motif is required to deliver the oomycete proteins into the cells of their respective plant hosts. The motif has provided a signature to search for other proteins that are delivered inside host cells, where they may be exposed to defence surveillance systems. In this proposal we aim to identify the entire complement of such proteins from P. infestans. We will characterize these proteins to seek those that are essential for infection (and thus are not easily lost by the pathogen) and those that show little sequence variation in diverse strains of the pathogen (and thus appear to be under selective pressure to remain unchanged). We postulate that such proteins represent potential Achilles' Heels for the pathogen if resistances can be found that recognize them. To this end, we will search in a wild potato biodiversity collection at SCRI (The Commonwealth Potato Collection) for plants that are resistant to these proteins (and thus to most, if not all, strains of P. infestans). These resistances are likely to be highly durable and thus will be prioritized for introduction into cultivated potato in commercially supported breeding programmes at SCRI. The second 'Achilles' Heel' of P. infestans that we intend to exploit is the machinery required for translocation of these virulence proteins inside potato cells. The translocation machinery is potentially a very suitable target for disease control, since inhibition of this delivery process would prevent effector proteins entering host cells and thus inhibit the pathogen's normal infection process. Experiments will be conducted to find the proteins responsible for translocation by identifying proteins that bind to the conserved delivery motif. We will conduct experiments to determine how they work. Mimicks of these proteins which bind to the delivery motif in oomycete virulence proteins will potentially not only prevent P. infestans from causing infection but will have a wider application by inhibiting other oomycete plant pathogens and will possibly extend to unrelated pathogens such as malaria. The biotechnology company Syngenta is the end-user that will evaluate the use of our findings in this aspect of the project.

The aim of this project is to characterise those genes that are responsible for the inception of pathogenicity by Globodera pallida. The British Potato Council estimates the UK potato production, processing and retail markets to be worth c. £3 billion p.a. and the potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are the most economically important nematode problems of this industry. They occur in 65% of UK potato land with G. pallida present at 92% of these sites. PCN impose an annual cost in excess of £50 million on UK potato growers and threaten the future of the crop for many growers. Breeding for resistance since the mid 1950s has produced few commercially acceptable varieties with resistance to G. pallida. Currently used chemical control methods are under increasing pressure due to cost, environmental and health concerns and there are no benign alternatives to the currently used compounds. Control of G. pallida is an essential requirement to maintain the competitiveness of U.K. production. For example, the consumer demand for food with no pesticide residues has resulted in Waitrose sourcing all its potatoes from crops that have not received a nematicide treatment (www.waitrose.com). This requires imports from countries with a lower PCN incidence or requires a more extensive agricultural system in the UK. Consumer support is likely for UK produce that avoids pesticide residues or environmental harm and is soundly based on a sustainable approach. This proposal underpins the innovation needed to reach that outcome. G. pallida must live as a parasite in plants. It has a complex interaction with its plant host. Second stage juvenile nematodes (J2) hatch from eggs in the soil, upon detecting a host growing nearby, then locate and subsequently invade the roots of the host. The J2 migrates inside the root and selects a single cell that it transforms into a large multinucleate feeding cell. Profound changes in plant cell structure and gene expression are induced by the nematode in establishing the feeding site. The nematode is known to spit into the cell. A few components of this spit are known to alter plant cellular development. In this proposal we aim to undertake a broad characterisation of putative pathogenicity proteins that cause the changes in plant physiology and that are therefore responsible for feeding site induction. We will determine if the putative pathogenicity proteins are produced in the glands of the nematode that secrete their 'spit'. The timing of the proteins' manufacture relative to the lifecycle of the nematode and its interaction with the plant will be measured to determine if they are required at the beginning of the interaction between the nematode and the plant, or continuously throughout the interaction. We will utilise high throughput fluorescent assays to determine if the putative pathogenicity proteins cause the nuclei of plant cells to increase in size - a common observable phenomenon in nematode feeding sites. We will also determine if the proteins can suppress host defence responses. Analysis will reveal what components of the plant cell the putative pathogenicity proteins interact with and then to ensure that the interaction has biological relevance components will be linked to one half of a fluorescent marker protein and co-transformed into plants. The marker protein does not produce fluorescence when it is split into N and C-terminal halves. Each half will be fused to one of the two putative interacting partners. This will lead to restoration of fluorescence within a cell if the nematode and plant proteins interact and reconstitute the split fluorescent protein. The advantage of this technique over other methods of visualizing protein-protein interactions is that it gives an indication of cellular localization of the complex, as well as interaction.

Modern biology is becoming more and more multidisciplinary. This is especially the case for the area of 'Systems Biology', which aims to predict how the different biological processes interact to result in a functional organism. These processes include the transcription of DNA into RNA, which codes for amino acids that make up the proteins, as well as the levels of hormones and metabolites that affect the biological processes. In the proposed network, we address how variation at the DNA level affects the transcription of DNA into RNA and how this then affects the characteristics of the whole organism. The aim is to reconstruct the networks that describe how genes interact. While conceptually straightforward, the area of research requires integration between biology, computer science (bioinformatics) and mathematics. At present, there is already some level of integration between researchers in these areas, but a lot of work is done in isolation. In the proposed network we will bring together: 1) biological research in plants, animals and humans. 2) Bioinformatics research which covers databases that contain known information on gene networks but also translates novel statistical and mathematical models into user-friendly software. 3) Mathematical biology, focussed on the methods of reverse-engineering of gene regulatory network, from a variety of experiments. The network will achieve its goal of further integration by organising annual meetings. These meetings will consist of an interactive workshop followed by a scientific conference. The workshop will provide ample opportunity for training of young researchers, dissemination of 'best practise' and new software tools and initiation of new collaborative research. The Conference will disseminate the cutting edge of the research area to the wider community.

Atmospheric carbon dioxide concentrations are predicted to rise to 550ppm by 2050 with concomitant increases in plant productivity. Such predictions seldom account for plant-insect interactions that under climate change may undermine projected increases in primary production by altering plant resistance to herbivory. This has potentially major implications for future food security. Climate change has the potential to modulate plant resistance to herbivory. Elevated CO2 concentrations (eCO2) have been shown to compromise both direct and indirect plant defences to insect herbivores, for example, by down regulation of plant resistance genes leading to enhanced herbivore performance. In many agro-ecosystems, plant defences arise through selective breeding which means plants are unable to adapt resistance mechanisms quickly enough to counteract the compromising effects of eCO2. Moreover, it remains unclear how higher trophic levels will respond to increases in herbivore abundance when plant defences are compromised. Using a multi-trophic system comprising red raspberry (Rubus idaeus), the large raspberry aphid (Amphorophora idaei), a predatory ladybird (Coccinella septempunctata) and an aphid parasitoid (Aphidus ervi), this PhD will investigate the effects of eCO2 on multi-trophic interactions, and specifically plant defence breakdown. Amphorophora idaei is the most significant pest (virus vector) of raspberry production in Europe. Plant resistance to aphid feeding in raspberry cultivars is underpinned by A1 and A10 genes, with A10 conferring stronger resistance, probably through altered leaf wax composition. Preliminary findings suggest aphids overcome resistance in raspberry under eCO2 because of altered gene expression. This project aims to: (1) characterise the effects of eCO2 on plant resistance to different aphid biotypes and identify which genes are implicated; (2) measure the phenotypic changes in plant defence mechanisms underpinning resistance breakdown; and (3) determine how population dynamics of higher trophic levels are affected by climate-induced changes in herbivore abundance. With experimental microcosms in controlled environment facilities, this project will test whether: Hypothesis 1: eCO2 accelerates resistance breakdown, with partially adapted aphid biotypes responding most rapidly to the down-regulation of resistance genes; Hypothesis 2: eCO2 alters composition of leaf waxes associated with aphid resistance; and Hypothesis 3: predator and parasitoid populations will follow a time-lagged increase corresponding to larger aphid populations under eCO2, but mutual interference will impede foraging behaviour at highest aphid densities. This PhD proposal is strongly aligned to the NERC Open Case Priority area of Agrifood research, with particular emphasis on the effects of climate change on proliferation of pests through resistance breakdown in a model crop. The impact of this study will be to provide mechanistic evidence of how multi-trophic interactions are likely to alter under climate change. This will enable crop breeders to target particular plant resistance traits and biocontrol measures for the adaptation and 'future proofing' of crop production under climate change. This contributes directly to the NERC Strategic Plan to enable society to respond urgently to global climate change. The project will meet key objectives of LWEC by investigating how climate change will affect crop-herbivore-enemy interactions and provide timely evidence-based recommendations to policy makers charged with climate change adaptation and mitigation.

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.